<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.18"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>NINJA: Class Members - Enumerator</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtreedata.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  <td id="projectalign" style="padding-left: 0.5em;">
   <div id="projectname">NINJA
   &#160;<span id="projectnumber">2.x</span>
   </div>
  </td>
 </tr>
 </tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.18 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(function() {
  initMenu('',true,false,'search.php','Search');
  $(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
  <div id="nav-tree">
    <div id="nav-tree-contents">
      <div id="nav-sync" class="sync"></div>
    </div>
  </div>
  <div id="splitbar" style="-moz-user-select:none;" 
       class="ui-resizable-handle">
  </div>
</div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(document).ready(function(){initNavTree('functions_eval.html',''); initResizable(); });
/* @license-end */
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>

<div class="contents">
&#160;

<h3><a id="index_a"></a>- a -</h3><ul>
<li>alignment
: <a class="el" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a">ArgumentHandler</a>
, <a class="el" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a5496170f117c3d558853e10ccee02666">TreeBuilderManager</a>
</li>
<li>amino
: <a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87abf0a7e58c2a951cb200e05ceed789d48">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7cad0f2f6fb9391cbe99f3f7b9dc4cfd63a">DistanceCalculator</a>
, <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7acae42440ed46d49841a42325c14aaf41">SequenceFileReader</a>
, <a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a089be0a828fca4605323da2e3a171202">TreeBuilderManager</a>
</li>
</ul>


<h3><a id="index_d"></a>- d -</h3><ul>
<li>dist
: <a class="el" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6a1af730d3ffbdc6354d6bda2549356cef">ArgumentHandler</a>
, <a class="el" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a19cba20113304d5be5b0b1b3cdb11b91">TreeBuilderManager</a>
</li>
<li>distance
: <a class="el" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aa9d20bc1085ccd1932c0ffd1d97a10dc6">ArgumentHandler</a>
, <a class="el" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a6d9503e62c1cc7af8faafe95ca03fa9f">TreeBuilderManager</a>
</li>
<li>dna
: <a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87af8d1253b6d8eecce0eea5eff86ddc63e">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7cafb040d095728a3f8116779a3cd63b2af">DistanceCalculator</a>
, <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7aeafabf791da5b60629a8c2eea71c9ee1">SequenceFileReader</a>
, <a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a9cf0eb2046097228c5269e9da5e47cba">TreeBuilderManager</a>
</li>
</ul>


<h3><a id="index_f"></a>- f -</h3><ul>
<li>fasta
: <a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a04f278c472cd9257e9f801c8094076a2">SequenceFileReader</a>
</li>
<li>FastTree
: <a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afdab094fe12b9abab259fbf519b9e3399a3">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a82d5f2ef688449e3584c82448b739b88">DistanceCalculator</a>
, <a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da7bff75f1893babce718611848369ad04">TreeBuilderManager</a>
</li>
</ul>


<h3><a id="index_j"></a>- j -</h3><ul>
<li>JukesCantor
: <a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda73811e507c334774db6b1ab687639b5f">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609aeb17fea69ad9aef888f2419a2814abf9">DistanceCalculator</a>
, <a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da78e91f6ce40102b0d61e8b9d51750638">TreeBuilderManager</a>
</li>
</ul>


<h3><a id="index_k"></a>- k -</h3><ul>
<li>Kimura2
: <a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda543fa5f6ad05da7f2efa6cefee5ba8d9">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a08d9cb898efb2c44ad9fd7b09d6c7e50">DistanceCalculator</a>
, <a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8dae1e7c68b84de2d982d8fc029b480cc17">TreeBuilderManager</a>
</li>
</ul>


<h3><a id="index_n"></a>- n -</h3><ul>
<li>none
: <a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda2c1d7a65ead4fefe3d70bfc2f64662e0">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a4f1b606366478e0f0f4c8acd4de71583">DistanceCalculator</a>
, <a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8daa48e32132856572cccb189cd72e521c7">TreeBuilderManager</a>
</li>
<li>not_assigned
: <a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda3bc78094126089bb7a17ff4a5ef7e60f">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a5f3b3cb6619f0d29daf2ff29a772d93c">DistanceCalculator</a>
, <a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da6a180df7a39a3dd2e0f2283fbdc9c9eb">TreeBuilderManager</a>
</li>
<li>null
: <a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87a340fde3e9bbd6b4f6450c7e10baa63a4">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7ca36b2c09e572187e6f03fa8bde6fda574">DistanceCalculator</a>
, <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7a9388aafb7eda9f884eed4c4dc315cc24">SequenceFileReader</a>
, <a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a229d43ec692cb711e87fa15d1a163c4a">TreeBuilderManager</a>
</li>
</ul>


<h3><a id="index_s"></a>- s -</h3><ul>
<li>stockholm
: <a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a71d055fafc2c7e7bda14e4aa68119a9c">SequenceFileReader</a>
</li>
</ul>


<h3><a id="index_t"></a>- t -</h3><ul>
<li>tree
: <a class="el" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6ab25e481414af792cbeffe6f6e2f06301">ArgumentHandler</a>
, <a class="el" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a432f48fbf28ef0573a1a3848b5cf1d40">TreeBuilderManager</a>
</li>
</ul>
</div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
  <ul>
    <li class="footer">Generated by
    <a href="http://www.doxygen.org/index.html">
    <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.18 </li>
  </ul>
</div>
</body>
</html>
